It is increasingly recognized that humans and other animals are multi-organismal, being comprised of co-evolved animal cells and microbial cells. The implications are profound. For example, interactions with pathogens are just a small subset of the diversity of animal-microbe interactions, and human health can only be understood fully in the context of the resident microbiota. This growing appreciation of the ubiquity and importance of beneficial microbes is both contributing to, and builds on, remarkable advances in our capacity to determine the diversity and function of complex microbial communities, especially through advanced sequencing methods and other emerging technologies. The impacts of this research include a re-evaluation of the nature of animal-microbe interactions and numerous opportunities for novel therapies to promote human health. The 2016 Beneficial Microbes Conference will provide a forum for the exchange of the latest conceptual and technological developments in this fast-moving field. It will provide an overview of the current state of research and future directions of inquiry, achieved by bringing together US and international researchers from multiple disciplines (microbiology, immunology, developmental biology, genomics, nutrition, ecology, systems biology, evolutionary biology and clinical science) who study a diversity of associations. The American Society for Microbiology (ASM) has generously provided core sponsorship, and the meeting will be held in Seattle, Washington on September 9-12, 2016. The meeting has six sessions: (1) Beneficial Microbes in Human Health and Disease Dynamics, to identify the causal roles of microbiota in promoting health and influencing susceptibility to disease; (2) Evolutionary Dynamics of Host- Microbe Interactions, especially how coevolution among microbes and between host & microbes can shape host-microbial interactions; (3) Role of Microbiota on Development will investigate mechanisms by which microorganisms influence organ, tissue and cellular development; (4) The Ecology of Host-Microbe Interactions will apply principles of population ecology and community ecology to explain and predict the composition and function of host-associated microbial communities; (5) Host Defenses Shaping Microbiota will explore interactions between microbiota and the immune/defense systems that lead to the formation of host-associated microbial communities; (6) Host- Microbe Signaling will explore the molecular mechanisms by which hosts and their associated microbiota communicate. Each session will include two invited talks and up to four talks selected from submitted abstracts. The conference will include advertised opportunities for break-out groups to discuss specific topics. Invitations and travel funds will ensure that early-career researchers, women and minorities are well represented among speakers and all participants.